Doctor Who  Guess Whoove?
by DoctorWhoofFanFics
Summary: The Doctor crash lands in Equestria, and not only is he a pony, but after an encounter with a certain purple pony he's now part of an elaborate scheme by one the Doctor's past foe. PS, my first fanfic. Hope you enjoy it
1. Doctor Who?

**NOTES FROM THE AUTHOR (thats me)**

**Still working on this, but doing it slowly cause of school starting and whatnot. First chapter is boring, yes i know. This is my first fanfic, soo... yea... lol. Hope you enjoy it though, once i finish the rest of this one.**

"GERONIMO!" shouted the brown colt, as he smashed the button with his front hooves. The seven mares watched in horror at what the brown colt had just done, and they faced forward, looking to see the consequences of his action.

* * *

><p><em>Oh no! I'm can't be late! Not today! This is not good... this is not go- Oof!<em> The purple mare was broken out of her train of thought when she collided facefirst into a tree.

"Wha... can't..be...late...flu..." she muttered in a daze. She dusted herself up and looked at the tree she had hit. "Ow... I have got to pay more attention...", the mare, was no other than Twilight Sparkle, who was soon aware of a strange wheezing noise. She looked in disbelief at what was transpiring in front of her.

_WHOOEeeeeee... WHOOOOEEEEEeeeeeee... Whoooooeeeeeeeeeewhoooeeehe... _

Suddenly, a mysterious blue box with the words `Police Public Call Box` written on the top materialized in front of her. The confused mare did nothing but look, mouth gaping.

"Ok... Obviously, I hit my head too hard... there's no way in Equestria that just happened."

Yet the box remained. Twilight shook her head, rubbed her eyes, did everything she could to try to get out of the daze. When nothing worked, she in charged at the box, expecting to fly right through it. Just as she was about to collide into the box, a door opened and a light brown colt with a coffee colored mane and an hourglass cutiemark stepped out.

"Ohhh this is brilliant. Hooves! Never had hooves before. Wait... how do I tie my bow ties now? But still! Hooves! Oh look a local...wait... STOP! STOPPPPPP - Ooof!" shouted the colt in a vain attempt to stop the incoming Twilight. Twilight smashed into the poor pony face first, her horn barely impaling him, with his hooves on the door the only thing stopping them from flying into the box. "This...ergg... would be soo much...ughhhh...easier...with HANDS!", he grunted as the momentum of the purple pony's charge wore off. Soon, the chargin' pony fell.

"Oh... my head..."

"You think you've got it bad? I just took a pony to the _**gut! **_Mind you, you should watch where you point that thing..." he said, looking at the unicorn's horn.

"Haha... you talk funny... like Rarity..." Twilight said, obviously disoriented.

"Yes, I talk funny, I always talk funny. I'm the king of talking funny.", the brown colt paused. "And that is _not_ how I'm introducing myself."

She grabbed her head and gave it a good shake. "That's better. Oh... right.. sorry about that. I'm Twilight Sparkle. Who would you be?"

"I'm the Doctor. Call me the Doctor."

"Doctor Who?"

The Doctor chuckled lightly at the question, as if he's heard it a thousand times before. "Just the Doctor, my dear. Say, mind my asking, but have you got an apple? Been craving an apple, not sure why... last time I had an apple I didn't really ..." he began rambling.

"Uhhh sure..." Twilight interrupted, grabbing an apple off an orchard with her magic. "Here you go, Doctor.", she said as she handed him the apple.

He took it, watching her strangely. He took a bite and immediately dropped it, flinching for a second. "Echh...same thing happened last time with Pond... Oh right, excuse my idiocy, but where are we?"

"Umm we're in Ponyville. I was just on my way to the Sugarcube Corner. If you'd excuse me, I'm in a hurry."

"Why? What's happened?", he said, staring at Twilight.

"Well... something's been happening to the ponies in the town. They've all come down with something. We've had them locked inside most of their homes, but the majority is locked inside the Sugarcube Corner. The one's who haven't been infected are trying their best to help cure them, and I'm in charge of find a spell to heal them."

"Okay... Come along, Sparkle!"

"What? But I don't even-"  
>"Allons-Y! Well, there's something I haven't said for a while. Doesn't sound right anymore does it..." The Doctor began rambling again. Sighing, the purple mare lead the Doctor to Sugarcube Corner against her better judgement.<p>

_If he is a Doctor... maybe he can help them_ she thought, hope beginning to fill her head.

* * *

><p>"If your a Doctor, why does your box say 'Police'? And why does your box randomly appear out of <em><strong>thin air<strong>_?"

"That's... rather hard to explain, Twilight Sparkle. First off, it's not just a box, it's the TARDIS. Second... well, that's how it travels."

"You.. travel in a box. What's wrong with hooves? Traveling in a small box... doesn't seem right."

"Right... small...box...definitely **not** bigger on the inside..."

Twilight seemed oblivious to what the Doctor was refering to, instead commenting on his behaviour. "Traveling in boxes..." she repeated. "Here I thought you were just some madcolt with a box." she said sarcasticly.

The Doctor stopped, and faced his new companion. "Twilight Sparkle, there's something you'd better understand about me, cause it's very important, and one day your life may depend on it... I am _definitely_ a madcolt with a box."

"Ok..." she said, turning forward. "Oh we're here!" The purple pony opened the door to the once happy building.

"Hey ther' Twi'. Who's yer friend?" Greeted Applejack, who was watching a door, indicated with a poorly written sign as _The Infected_.

"Hey Aj, this is the Doctor. He's going to help us find a cure to this disease."

"Really! That's great news! Pleased to make yer accquanitence ther' Doc'!" Applejack said, excitingly shaking the Doctor's hooves.

By the time Applejack was done shaking hooves, the Doctor was blowing on his, sore from the ordeal. "Hello to you too. May I say, I am loving your hat. I've got a knack for unusal hats myself. Ever heard of a fez?"

"No... but I like yer' tiethingy on yer neck."

"Yes, well bow ties are cool."

Twilight casted him a glare, reminding him of is goal.

"Oh, right! Let's see what the problem is!". The two lead him to a secured room, where an infected patient slept on a table, chains restricting his hooves and tail. The colt was hooked up with medical equipment, and all around they beeped and hummed.

The Doctor had taken out a strange pen like-device, which had metal claws at the end and a green light. "Ok... this might be a tad bit difficult... seeing as we have no fingers and all.. Ah! I got it! Nrow, iwf ir cawn jwst... twere!" The Doctor had put the device into his mouth, which he bit down on. The green light ignited, and a strange humming sound could be heard. He pointed it to the patient and clicked and held the button multiple times, seemingly scanning the entire patient in various places. He spat the device out onto his hand and looked at the results. "Oh no... this is bad. This is very, very bad." He did a complete spin, and faced the two mares behind him. "EVERYBODY OUT! Out Out Out out OUT!" He gestured them out quickly, exiting and closing the metal door. He pulled out his pen again, and fiddled with it. Getting a grasp, he hit the button, and pointed it around the door. "That should hold it."

"Doc, what's goin' on? Yer actin' like there ain't no apples left in the orchard!" asked Applejack.

"That pers... pony is infected by some sort of modified Nanogenes. I don't understand..."

"What Doctor? You don't understand what these Nanothingies are?"

"No... I've seen this happen before. No, what I don't understand, Twilight Sparkle, is how they wounded up here! These seem to be based off of Chula Nanogenes, yet there are some sort of... wibby wobbly.. stuff... in there as well. The problem here is that pony is extremely infectous! Any contact with him will instantly infect you!"

"So what do we do Doc'? We can't treat 'em if they can get us sick in one touch!" asked Applejack, beginning to worry.

"Ok...ok...here's what we do. Gather up the rest of the uninfected and get them back to the Tardis." The Doctor said, as he pushed Twilight and Aj towards he door. "If I'm not in there , wait outside the Tardis. I'll meet up with you soon."

"Wait, where are you going?"

"No time, GO!"

The two mares left hurriedly, gathering the rest of the healthy ponies. The Doctor began walking to the sealed door. Staring at the metal door, he slid open a hatch. "Hello. I'm the Doctor. I can help you. But first, you need to tell me what you want."

The body remained still, no signs indicating that it had heard what the Doctor said.

"Come on, I know you can hear me. So WAKE UP!" He roared.

The patient's eyes snapped open. It looked at the Doctor, and began to speak. "Muffins..."

"Brilliant! Your talking! Talking's good. Now, do you remember your name?"

"MUFFINS."

"I...guess not. Right. Can you give me anything to work with? Anything at all?"

"MUFFINS! MUFFFINNNNS!"

The Doctor was suddenly aware of a banging behind him. He looked to see a basement door break, showing the faces of the other infected. "Not... good." The infected began smashing through the remainder of the door, with cries of muffins and crossed eyed expressions. They soon began to descend upon the Doctor, attempting to grab him. "Whoa! Wait, let's go back to talking! Talk, talk to me! Talk to the Doctor! Whatever your looking for I can - Whoaaa!" The Doctor said, as he narrowly avoided being hit by an infected. "Right... Well... If you would all just STOP for a minute, then maybe I can tell you.." The Doctor stepped infront of the door, trying to coax the crowd of ponies to listen, yet to no avail. "Never, let me talk." He ran outside the Sugarcube Corner, stopping to sonic the door shut. "That... should hold them for a few minutes. Now, lets see how the purple mare's done."

* * *

><p>"Twilight, umm, I don't mean to bother you are anything, but um, can you tell us what we're doing here, if you don't mind?" squeeked Fluttershy. The purple pony looked around, trying desperately to figure out how to tell Fluttershy the news. The only ponies that were still healthy was Twilight's best friends, Rainbow Dash, Fluttershy, Rarity and her assistant, Spike, a baby dragon. There was also Scootaloo, Applebloom and Sweetie Belle, and Big Macintosh.<p>

"Umm well, you see uhh - " she started, cut off as she heard someone yell from behind a hill.

"Twilight, are these the last healthy ponies?" The Doctor asked, appearing from the direction of the shout.

"Uh yes, these are the last healthy ponies we could find."

"Good. Now, everypony, into the Tardis!" said the Doctor, as he snapped his hooves together (which wasn't quite the easiest thing.), causing the Tardis door to open. He quickly gestured them all in, against their cries of the box being too small. Inside, everypony was dumbstruck by the size of the box.

"Yes, yes, bigger on the inside! There's no time to go out and check, just take my word for it!" he shouted, running to the controls, flipping switches and levers. Meanwhile the rest of the ponies were running around investigating the Tardis.

"This place has a swimming pool?" exclaimed Rainbow Dash.

"There's enough room here to fit two Sweet Apple Acres!" said Applejack in disbelief.

"This library's huge! I've never seen so many books before!" Screamed Twilight in excitement, as she set the sleeping Spike on to a cloth covered basket. The other ponies continued making remarks about the size of the Tardis, except for Fluttershy. She just stood there quietly, staring at the Doctor.

As he finished flipping the last of the switches, he turned to run towards a panel, only to stop and walk backwards to Fluttershy. "Why aren't you exploring the Tardis like your other pony friends?" He asked, curious.

"Well..um...if you don't mind..I'd just like to stay here umm if it's no problem with you."

"No, none at all! Your free to do whatever you please, Ms...?"

"I'm Fluttershy." She finished shyly.

"Fluttershy, brilliant name! Call me the Doctor, I call myself the Doctor so you should call me the Doctor. Not sure why I call myself the Doctor though, but it was that or being called the rotmeister. Don't call me that, that's not a very good name, so just stick with the Doctor.", he finished, grinning at Fluttershy.

She returned his grin with a small one of her own, and after a few minutes of akward silence between the two, she asked the Doctor a question. "Umm if you don't mind answering Doctor, what are we doing now?"

"Well, I've transferred the Tardis into the atomosphere. It'll give us time for me to think of a way to fix this. Basicly, what's going on here is we're in a bit of a jam. That reminds me, have you got Jammie Dodgers here? No? That's rather unpleasant...Oh? Right yes the situation at hand. The nanogenes were modified to act differently, probably by impact or the energy wave that turned me into a.. oh, right. Anyways, the resulting nanogenes came in contact with somepony, infecting it in a randomized amount of time. These nanogenes were meant to repair alien bodies, so they've never had any contact with ponies. They don't know what your species suppose to even look like. They took the nearest pony around them, and used them as the template. What I don't understand is why these ponies insist on muffins...".

"Did somebody say muffins?", shouted a pink pony excitingly. "I love muffins! Almost as much as I love cupcakes, and cakes, and cookies!" The ecstatic pony continued, as she bounced up and down. "You're a new pony aren't you? Cause I haven't seen you before, and I know ALL the ponies around here! I'm Pinkie Pie! What's your name? Where do you come from, what's your favourite food, do you like parties? Will you be my friend?"

The Doctor stared at her for a second, trying to make sense of the questions. "Hello Pinkie Pie! Doctor, Galifrey..though i suppose Galopfrey would be an appropiate name now, definitely not yogurt...it's stuff with bits in it, Yes, and yes!"

"Oh Goodie! New friends! Let's have a party to celebrate!"

"Now's probably not the best time, Pinkie Pie. I have got to figure out why the sick are so obsessed with muffins..." the Doctor thought, trying to make sense of the situation at hand. "Pinkie Pie, gather the others, I am going to new some information...".

"Okey Dokey Lokee!" Said the pink pony, as she hopped further into the Tardis halls.

A couple of minutes later, the other ponies were gathered around at the control panel. "Ok, first thing's first. I'm the Doctor, and you have got a problem. There are muffin crazed ponies out there, and I don't have the slightest idea why. To find out why, I'm going to need your help. Now since we are going to see each other for a while, it might help to know the names of the rest of you."

The ponies called there names one by one, until all names had been said and done. "Right, now that we're all formally introduced, here's the problem." He explained the nanogene problem to the ponies, who were barely able to grasp the gist of what he was saying. "Is there some sort of medical records, anything about the first patient? Some pony note, a stamp, anything?".

Twilight spoke up. "If there are any forms, then Nurse Redheart would have had them in her office."

"Perfect! Where is that?"

"It's a bit past the Library."

"Good. Let's go!" He paused, looking at the screen. "Which one's the library?"

"Big tree."

"This library is a big tree?"

"Also my home." Twilight added, a bit offended.

"If you live in a tree, where do the Berenstain Bears live?" He added humorously.

"The who?"

"C'mon, you haven't heard of the Berenstain Bears? You know, talking big brown bears who live in trees?... nevermind. Hold on tight everypony, this ride is going to get rough!" The Doctor pulled the lever, and the Tardis started wheezing. The inside shook slightly, alarming the ponies. A second later, it appeared in Ponyville, a few minutes away from the Library. The Doctor asked the Cutie Mark Crusaders to stay in the Tardis, to accompany the sleeping Spike, and to keep them out of harm's way. "Maybe you can be Tardis watchers?", he suggested jokely, though they took his suggestion to heart and began talking excitingly about it. The rest of the group exited the Tardis, leaving the fillies alone with Spike and Fluttershy, who stayed behind to watch them.

"Follow me, don't stray from the group." The Doctor began walking, only to be stopped by a huge stallion named Big Macintosh.

"Uh, nurse's place is thataway."

"That way?"

"Eeeyup."

"Righttt, my mistake. This way ponies!"

Minutes later they appeared at the nurse station. "Door's locked... now problem for the sonic!" The Doctor said, as he pulled out his sonic screwdriver once more.

"What's do you have there, darling?" asked Rarity.

"Sonic Screwdriver! Great for opening doors!" He said, as he toggled the device. He pushed the handle and propped the door, allowing the group to enter first.

"Everypony, find some sort of medical paper with a date of infection. Say, what ever happened to the nurses that worked here?".

Everypony stopped as the pondered the thought. They haven't seen the nurses at all after the first week when the disease first hit. They suddenly became aware of a hard panting sound, followed up a distorted voice. "M...uffins...".

"Not good..." the Doctor thought outloud.

The two nurse's bodies rose from behind a counter, both with the same crossed eyed expression.

"Those are some crazy-tastic eyes!" exclaimed Pinkie Pie, oblivious to the situation. She began walking forward to get a better look, when she was stopped by the Doctor.

"Don't get too close, Ms. Pie, or those eyes will be the last thing you see for a while." he warned. "Everyone, out where we came from!". He rushed over to the door, opening it, only to slam it shut again. "Not good... the others seem to know we're here."

"How do you know that Doc'?", asked Applejack

"Call it a hunch." he said, as the front door thrusted over, revealing the mob of muffin crazed zom-ponies.

"Ideas, anybody?" he looked around, nobody saying anything. "Up to me then. Come on, there's got to be something...HA! I got it!" he exclaimed, as he soniced a nearby lamp. The lamp exploded, yet the sick ponies continued.

"Great job, maybe they're scared of the dark.", Rainbow Dash comment sarcasticly. She began backing up from the oncoming swarm, tripping on a handle in the ground. "Ouch! Huh? Hey Doc, there's some kind of cellar thing here! It's locked though."

The Doctor ran towards Rainbow Dash and looked at the cellar. He clicked the sonic screwdriver, attempting the unlock it.

"This door is wood isn't it?". The other ponies nodded. "Then we've got a problem. My sonics screwdriver doesn't work on wood...".

"What! What kind of lame alien tool pen can't work on wood?" critiqued Rainbow Dash.

"Oi! Don't diss the sonic! I love my sonic! There's got to be another way..."

Applejack stepped up. "Allow me." she quickly bucked the door a few times and pretty soon it gave way. "Years of applebucking." she said proudly.

"Good job littl' sis'." commented Big Macintosh.

"Oh you brilliant pony you!" complimented The Doctor. "Now, unless you feel like hunted muffins with crossed eyes, we'd better hurry!" he warned. Something suddenly caught his eyes. He noticed a clipboard with numbers and statistics.

"Doctor! Don't!", warned Rainbow Dash. He ignored her warnings and dashed to the clipboard, barely managing to reach it in time. Soon the infected ponies were almost upon him. He jumped into the cellar right before Twilight sealed the doors, in an attempt to buy them some time.

* * *

><p>The cellar was dark, and smelled of herbs and spices.<p>

"Wait right here...", called the Doctor, who disappeared somewhere. The six ponies waited, wondering what happened next. Suddenly, a severed face appeared in the air infront of them. They all screamed, excluding Big Macintosh, who simply looked on.

"Oh.. sorry... I was getting my fez..." apologized the Doctor. He fiddled with his sonic screwdriver, and aimed it around. "Should be a light switch somewhere.. Ha!". The room was instantly lit, revealing the Doctor's bright red hat. The mares looked at the hat in complete astonishment, and burst out laughing, followed by Bic Macintosh's signature 'Eeyup'.

Rarity looked at the hat with disgust. "Ugh, that hat is simply not right for you! And that bow tie! If that isn't a cry for help, I don't know what is!"

"Oi! What's wrong with bow ties? Bow ties are cool. Fezzes too."

"Where did you even find that thing?" asked Twilight, confused at how it had appeared. She looked around the cellar. Aside from a few small holes, the only way out was behind them, yet the entrance was locked. _Oh great, we're also trapped._

"Nowhere you need to know, Twilight. So, ponies. Any thought on how we get out?"

"We thought you'd know, you bein' the one to lead us here." replied Applejack.

"Oooh I know! Maybe Twilight can magic us out!" said Pinkie Pie.

"I'm not so sure... I have a hard time teleporting just Spike and me out a few feet! That wall looks thicker than a few feet."

"Magic? Blimey... talking colorful ponies with magic. That's something you don't see everyday... maybe every two weeks or so, but not everyday. Hm... hold still for a minute Twilight." said the Doctor, as he began sonicing her. Looking at the results, he started sonicing everyone in the room. "Well thats strange... you lot are running off some high leveled radiation. Except for you Big Macintosh, you are a perfectly fine if not a bit rather large, pony."

"Eeeeeyup."

"So... what's with the high radiation? There seems to be a certain difference in the energy, each linking to one particular strand, which requires all other 5 energy sources, else the sixth will not activate. Who's the other pony we're missing?".

"Fluttershy! What your talking about is the Elements of Harmony. We're the Elements of Harmony." Twilight informed the Doctor.

"Elements of Harmony? Would you mind demonstrating it?"

"Sorry Doctor, but we can't. It requires all of us to do it, so we need Fluttershy. We also don't really know how to use it. The one time we did, it just sort of happened.", explained Twilight.

"Okkk... back to the current situation at hand. What were you saying, about magic and teleporting?"

"Oh, well I can use magic to teleport us out, but I'm not sure if I can get us all out in one peace... the wall looks pretty thick, and I can on teleport a few feet."

"I see... would you mind trying once?"

"I'll give it a shot." Twilight's horn suddenly glowed, and the same glowing aura surrounded the other ponies. The Doctor examined the aura, thinking. He was dimly aware of the sound of splintering wood, as the cellar door began to chip little by little.

"Twilight, I've got it! You can stop whatever your doing now!"

The light from Twilight's horn faded, along with the aura. She seemed a bit exhausted from the attempted, but shook it off.

"What your horn is doing Twilight, is manipulating and creating personal Huon particles. Your destination is filled with Huon particles, while your horn also adds and creates huon particles in your own body. With the large amount of the particles at your destination, it attracts the ones in your body, causing you to teleport. Haha! Brilliant!" he stated, while making seemly random hoof gestures.

"Ok... so what can we do about getting us out of here Doc'?", asked an impatient Rainbow Dash.

"I've got an idea, but I'm going to need Twilight's help."

"She'll do it! Hurry Twilight, I just CANNOT spend another second here, my glamorous hooves are getting all filthy!" cried a hysterical Rarity.

"Ok, Twilight, I want you to concentrate your magic into my sonic screwdriver when I say so, got it?" Twilight nodded. "Ok, ready...GO!" The Doctor activated his sonics screwdriver at the exact moment Twilight used the spell, causing the screwdriver to glow a deep red, with energy crackling at the edges. The cellar door was almost gone, being broken bit by bit by the infected.

"Doctor, are you sure this will work?" grunted Twilight.

"Haha, I have NO idea!" shouted the Doctor over the sonic's distorted sound.

"What! But, but what if something happens -"

"Twilight, you need to start trusting me, it's never been more important. If there's a time where you have to trust me, it's now!"

Twilight looked at the Doctor, struggling to decide. She has never seen this colt before, she has never met him until today. She had no reason to trust him, and certainly not with the lives of her friends. But she saw something in him, something she couldn't explain. She closed her eyes, and concentrated her magic into the screwdriver. _I hope your right, Doctor._

The Doctor pointed the screwdriver through a hole in the thick wall, then redirected it into the room. "I think it's working!". A strange buzzing noise started filling the air, and the sonic screwdriver shook in the Doctor's hooves, raw energy shooting out of it.

"My word, Doctor, is feeling rather... fuzzy so to say, normal?" asked Rarity.

"OOoh this tickles! Hahahaha!" laughed Pinkie Pie. Soon they were all glowing, and in a split second a huge blinding white light filled the room.

"GERONIMO!" cried the Doctor, as the light enveloped his body, seconds before the cellar door broke open.

* * *

><p>Outside the medical station, a good 20 metres away from the cellar, the group of ponies emergied. Night had descended, and the ponies were immbolized briefly by the magic. They got up, testing for any broken bones or bruises. Aside from a slight daze, it seemed they were all in one piece.<p>

When the dizziness subsided, the ponies discovered the Doctor, lying unconsious, and unaturally straight on the ground.

"Doctor! Doctor, are you okay?", demanded Twilight. She felt his heart beat, hearing none. "No... no Doctor, no!" cried the pony worriedly.

"I'm sorry Twi', but he's gone.", Applejack said, as she attempted to comfort Twilight.

"He may have been the only one able to stop whatever's happened."

As she got up, she thought she heard something. She looked at him, but seeing nothing changed, she went to join her friend.

"Gotchya."

All eyes turned towards the Doctor's body, which instantly sprung up. "Ha. Twilight Sparkle, crying over a stranger, a mysterious Doctor." he smiled.

"You... You... _Impossible _Colt!" Twilight screamed in sudden delight, running towards the Doctor, giving him a warm embrace, much to his supprise.

"There, there Sparkle. I'm alright!"

She didn't stop hugging him. Instead her hugs grew harder, becoming painful.

"Ughh... TwiL - Ooof! ight... that's really... starting to hurt."

"You had me thinking that you _died_! You were alive the whole time?", Twilight said, all signs of kindness gone.

"Okay, it was a bit stupid- GAH! OKAY! VERY STUPID! STUPID STUPID DOCTOR! BUT I REALLY COULDN'T GET...UGH.. UP! MY SECOND HEART STOPPED...AH!..BEATING!"

Twilight, in surprised dropped the Doctor. "Second heart? What? That's not possible! Ponies only have one heart!"

"I'm not a pony." said the Doctor, trying to catch his breath. "I'm a Timelord. Or... Timepony now. There's alot I haven't told you yet Twilight!"

"Your... an alien? But... but you look like a pony!"

"And you look like... well a pony. But you would look like a Timepony if we had any. We came first. As for my... nap.. it took a while to get my second heart back up and running, I have no idea how you ponies do it, just one heart! Now, if you're going to continue strangling me, I think I should solve your little problem first, wouldn't you agree?"

Twilight nodded, the original goal returning to her mind, and the rest of the other ponies' minds.

"Wait, so what was that thing you picked up?", asked Rainbow Dash.

"Dates. Dates of when the first sick pony checked into the medical station.", The Doctor replied, as he reached for the notes. He became aware of his charred Sonic Screwdriver in his hooves. "My screwdriver!"

"Uhh Doctor, I don't think now's the time to -"

"I love my screwdriver!"

"Doctor! Pay attention!"

"What? Oh right.", the Doctor said, quickly pocketing the screwdriver. He grabbed a slip of paper from his pocket. "Here, date Monday, August 12th, Equestrian Year 1001. Nearly a week ago. The name here is a Ms. Ditzy Doo? Anybody?".

"Ditzy? You mean Derpy?" asked Rainbow Dash.

"Hmm, Ditzy Doo must be Derpy's real name.", commented Applejack.

"Eeeeyup."

"Now that you mention it, Derpy Hooves does have those extra fantabulous crazyrific eyes that those other ponies had!" added in Pinkie Pie.

"Does anyone know where we can find this Derpy Hooves?"asked the Doctor.

"She resides along the edges of Ponyville. She use to bring letters to my boutique." said Rarity.

"Right then. Before we go to Ditzy Doo's, I require a favor from one of you. Earlier, you said that this 'Elements of Harmony' was some sort of giant wave of energy. You also said it required Fluttershy, the yellow mare that stayed behind if I remember right. I need one of you, preferably not another Element, do get her here. There might be a way to reverse all of this with the Elements of Harmony.", declared the Doctor.

"I'll do it.", offered Big Macintosh.

"One more thing, when you're in the Tardis, find as many metally bit box things you can find, and bring them to Ditzy's home." Big Macintosh nodded, and bid the others farewell.

"Good, now to Ditzy's home!" said the Doctor, as Big Macintosh proceeded back to the Tardis.

As they walked, Rarity questioned Twilight about the Doctor. "So, Twilight. Applejack tells me that you know this colt the longest?"

"Ummm yes? Why?"

"Well... I'm curious. Are you and him... together?"

Twilight stared, comprehending the question. "What! NO! NOOO! I just met him today! Why would we be... together?"

"Oh, Twilight, we all saw the way you acted when you thought he was dead. And I've seen looks on your face." smirked Rarity.

Twilight could feel her face burning. "No, we're just friends! No, not even friends! He's just... some mad colt!"

"Well, if you insist dear. If you're not into him, I guess you won't mind if I try? If it didn't strike you before, he's quite the looker, if I do say so myself. And that personality.", said Rarity, a tad bit dreamily. "Of course, he'll need a full makeover! That fez has got to go! And that bow tie..." she shuddered.

Twilight laughed. _Atleast my friends are still the same...somewhat _she thought to herself.

Atlast, they arrived at their destination. A big, steal lock sealed the front door. Obviously someone wanted the door to remain locked. The Doctor took out his sonic screwdriver. He clicked it, testing it. Slight sparks discharged in an arch from the sonic's head, but so far everything was working properly. He pointed it at the lock and toggled it, causing the mechanisms to spark and unlock.

"You can't do that! That's breaking and entering!", complained Twilight.

"What did I break? Sonicing and entering." The Doctor returned. "Wait, before we go some of you will have to stay out here and watch out for the big mob of infected. Any volunteers?"

"OOoh, Ooh!" shouted Pinkie as she jumped up and down waving her arm. "Dashie and I will do it!"

"Fine..." sighed Rainbow Dash.

"Good. Now come along Sparkle."

"Oh wait, I'm coming with you!" said Rarity.

"The more the merrier!" cheered the Doctor.

The inside of the house was dark, and rather dusty, making the place seem unused for days. Other than the low groans of disapproval by Rarity, there was no other noises.

"Is she always like this?", whispered the Doctor, amused.

"Rarity? Yes.. but don't take it as something bad. Though she's really uptight about neatness and appearance, inside she truly cares about others."

"If only some humans were like you ponies, my job would be a hundred times easier." The Doctor chuckled.

"Humans?" asked Twilight.

"Maybe I can show you one day. If you give me a chance. There's alot out there that I'm sure you'd love to see." he paused, allowing the information to sink in. "So how 'bout it Sparkle? Your friend's are welcomed too."

"Why me, Doctor? Why not ask Rarity? I'm sure she'd be very quick to accept the offer."

"Why not you? Maybe it's because -" the Doctor ended, stopping in his tracks, eyes widened.

"What's wrong?"

"That's impossble..."

Infront of the Doctor, there was a strange metallic-silver wall.. Looking hard through the shadows, Twilight discovered the wall held a strange symbol, one which resembled a cresent moon.

Rarity then caught up with the group, and discovered the symbol as well. "What is it Doctor?"

"...Cyberm-"

Suddenly, loud clanking sounds filled the room. The wall suddenly lifted, and a metalic pony appeared from it, with the same C carved on it's breastplate. With a horrible electronic voice, it spoke to the stunned Doctor. "I am the Cyberleader, and you will be deleted."

* * *

><p>To Be Continued.<p> 


	2. Iron Pony

The Doctor stared, mouth gaping. Then, to the complete astonishment of Twilight and Rarity, he started laughing. "Look at you! You're a pony! It's a pony!" he said, directing himself to the two mares, while continuously laughing.

"Silence. You will be deleted."

"Right... You're not the first one to try. There have been so many."

"My word, what is that horrible thing?" asked Rarity

"I don't know. Ha! Isn't that brilliant! In my universe, this thing is call a cyberman. But now... well, I'd say we should call it a Cyberpony." replied the Doctor, as he faced the silver metal pony. "Where are the other Cybermen?"

"I am the only one here."

"Why did you come alone?"

"The Cybermen did not choose this universe, The Emptiness did."

"The Emptiness? What's that?"

"Information on that subject is absent." The Cyberpony turned to the Doctor's group, scanning each one. It's gaze lingered on the brown colt.

Suddenly, a blaring sound emitted from behind the Cyberpony, followed by a severed metallic voice. "Total Infection at 85%. Initating phase Two." Suddenly, the room began shaking.

Cracks emerged on the floor, spreading quickly. "Resident lifeforms will be upgraded." Stated the Cyberpony. "You will be freed from your emotions and upgraded."

"Uhm... No." returned the Doctor.

"Doctor... What's it mean by 'upgrade'? Is that bad?" asked Twilight.

"Well... it means...you're going to be like that."

"Ewwww! I simply cannot look like _that_! The mane is horrid! And the colors! So dull!" said Rarity with a whining tone. "Doctor, please tell me you have some sort of plan."

"Well... I do. Basicly... " the floor around them began breaking off, falling into the dark abyss beneath them. "...RUN!"

The group of ponies clipclopped through the cracking house, with the Cyberpony following it. The Cyberpony gained on the group, firing red particle beams. The Doctor slowed, and grabbed a nearby fire iron. As he sparred with the Cyberpony, he slowly backed to the exit. A termor caused the iron pony to lose it's balance, allowing the Doctor to buck it away. Defeated, it abandoned the chase, disappearing into some secret passage. As the group of ponies exited, followed shortly by the Doctor, they were greeted by a shocked Rainbow Dash and an escatic Pinkie Pie.

"Oh boy oh boy! What's going on in there! Sounds like a party! Let's go and join it! I'm ready to Par-TAY!" declared a bouncing Pinkie Pie.

Rainbow Dash looked at Pinkie Pie and shook her head. "Doctor, what did you do! Did you find Ditzy Doo? What's up with the ho- " she started, unable to finish, as the roof of the home exploded into the air. A giant silver pole emerged from the ground, smashing through the remains of the house, towering over the startled ponies. It suddenly began beeping, sending off a wave of sound. Almost immediately, three pegasus ponies emerged from the gaping hole created by the antenae.

"Doctor! That's Ditzy Doo over there!" identifed Rainbow Dash, as she pointed her hoof to a grey pegasus with a blonde mane who circled the group.

The Doctor took out his sonic and activated it. Sparks flew from it, and the light emitting from the end flickered briefly before finally stablizing. "Don't let them touch you! One touch, and you're gone!"

The three pegasi flung themselves at the Doctor and his companions. Soon, they were about to make contact with them. At the last second, something whizzed by, smashing into the oncoming ponies, colliding with the nearest pegasus, knocking him back. Another object flew again, repeating the same procedure with the second pegasus, which was quickly followed by a barrage of similar circular objects.

"YEEEEEHAW! How do you folk lik' 'em apples?" Shouted Applejack, who appeared a few miles away. With her was a huge wagon piled high with apples of all colors. "Head's up! Here comes another!" she exclaimed, as she threw an apple eye in the air, and quickly bucked it, sending it flying faster than before.

"Applejack!" shouted the four mares with excitement.

"Keep yer head's down girls! You too, Doctor!" she added before winking at the colt.

Soon, the hostile pegasi were on the ground, beaten and covered with bits of apple.

"Now, is everypony alright?" asked Applejack. The mares all nodded, with the exception of the Doctor, who was looking at the antenae.

"...What does a big flashly lighty thing do?" he wonder outloud.

"Oooh ohh! I know! It's big and flashy, and it lights up!" cried out Pinkie Pie.

"Right... lets see... it beeps... makes sounds... sends signals... signals? Signals! That's it! It sends signals! This antenae is transmitting a signal to the nanogenes! From the looks of it, it's sending out high frequency modifying soundwaves attuned to the nanogenes' systems."

"Come again?" asked Rainbow Dash.

"Imagine a banana, or anything curved. Actually don't, cause it's not curved or like a banana. Forget the banana!"

"What's a banana?" whispered Applejack.

"It's a -"

"Muffins..." something cried out.

The Doctor turned towards the fallen pegasi. The one identified as Ditzy Doo began twitching. She got up on her hooves, barely standing. Immediately, the antenae began flashing a violent red, and the beeping intensified. Soon the other downed Pegasi were up, their eyes no longer twisted or crossed. They were pitchblack, and showed no signs of emotion. Ditzy Doo's eyes however were still quite derped, yet they were as dark as the others.

"Doctor, what are they doing?" asked Twilight.

Her question was answered by the three pegasi in union. "You are compatible." They began marching towards the Doctor and his friends, their movement almost mechanical, and their tone cold and emotionless.

"The Nanogenes are reacting the the signal... they're becoming like Cybermen!" said the Doctor. His answer was drowned out by the rest of the sound of moving hooves. Soon, everything infected pony was surrounding them, leaving the group at their mercy.

"You will be cyber-converted." they all stated. As the began to march forward, two things happened at once; A huge flash of light appeared near the group, and Big Macintosh arrived, pulling the Tardis, with Fluttershy and the Cutie Mark Crusaders inside.

The ponies ignored the red stallion and his luggage, instead resuming their original task. From the light, bolts of pure magic shot from it, hitting one of the ponies and knocking him unconcious.

"Twilight Sparkle, what is going on?" demanded a voice from the light, which materalized into the form of Princess Celestia. "My loyal subjects cannot act like this, what has happened?"

The Doctor, who looked at the princess, Applejack, and at the sight of the Tardis being pulled by a pony, mumbled, "Blimey...it's a long.. **long** story. But for starters, do not let them touch you."

The Princess' question was left unanswered, as they soon found themselves dangerously close to making contact with the other ponies. A pegasus lashed out at the royal alicorn, to which she responded with a powerful blast of magic, rendering the pegasus stunned. "Twilight, escape with your friends now!" she ordered, as she zapped another pony.

"She's right, run to the Tardis!" said the Doctor, as he brought his Sonic screwdriver to his hoof. The two ponies backed up into one another, and circled around, hitting the controlled ponies, creating a path for the other's to escape.

"What's that? A weapon?" grunted the Princess.

"No, Screwdriver. A sonic one." The Doctor replied.

"Then what are you doing here?"

"Helping!"

"You've got a screwdriver, go build a cabinet somewhere!" she looked to the direction of the Tardis. "Get them out of here, do not let these... things... get my faithful student or her friends."

"Right, on it." replied the Doctor, as he dashed towards the Tardis.

"Forgive me, my loyal subjects..." apologized Celestia, as she charged her magic. Her horn glowed bright yellow. She pointed her horn into the air, and released the concentrated magic. Multiply rays if it shot from the horn, hitting all the infected ponies surrounding her. Wave after wave of the ponies were knocked out, but there was no time to celebrate. Each pony that fell were replaced with ten more, and soon Celestia grew weak. Alas, she fended off the rest of the ponies, at the cost of most of her strength. She fell to the ground, panting for breath. Her weary eyes noticed a grey shape approaching her, and she focused her vision. The Cyberpony lumbering over her shocked her. She staggered to her feet, but quickly slipped down. The Cyberpony pointed towards her, and one of the downed ponies got up and gripped her hoof. A yellow, dust-like substance seeped from from the pony onto the Princess. She stared in horror at the nanogenes, unable to do anything about it. As she waited for the nanogenes, she realized they should have made contact by now. As she opened her eyes, she saw they floated around her, unable to move forward.

"You are not compatible. You will be deleted." explained the Cyberpony. It brought it's right hoof to Celestia, electricity coursing through it. Before it could kill her, the crack formed from the antenae spread, and using her last bit of strength, the Princess shot a wave of magic at it, causing the crack to ripple and spread. The entire ground soon shattered, leaving the Cyberpony and Celestia to fall. Utterly powerless, she closed her eyes and prepared to face death, her last thoughts were of Twilight and her own sister, Luna. Absolute darkness overtook her, and only a faint thud could be heard...


End file.
